Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTL on the Genetic Basis of Plant Height and Heading Date in Rice

Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plantheight and heading date, using a doubled-haploid ( DH) population consisting of 190 lines from the cross between anindica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A geneticlinkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach wasapplied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactionsinvolving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactionswere detected between the digenic interaction and environment. The amounts of variations explained by QTLs of maineffect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not bedisregarded.

Effects of erect panicle genotype and environment interactions on rice yield and yield components

The dense and erect panicle (EP) genotype conferred by DEP1 has been widely used in the breeding of high-yield Chinese japonica rice varieties.However,the breeding value of the EP genotype has rarely been determined at the plant population level.Therefore,the effects of the interaction of EP genotype and the environment at different locations and times on rice yield and its various components were investigated in this study.Two sets of near-isogenic lines (NILs)of EP and non-EP (NEP) genotypes with Liaojing 5 (LG5) and Akitakomachi (AKI) backgrounds were grown in the field in 2016 and 2017 in Shenyang,China,and Kyoto,Japan.In 2018,these sets were grown only in Kyoto,Japan.The average yields of the EP and NEP genotypes were 6.67 and 6.13 t ha^(-1)for the AKI background,and 6.66 and 6.58 t ha^(-1)for the LG5 background,respectively.The EP genotype positively affected panicle number (PN) and grain number per square meter (GNPM),mostly resulting in a positive effect on harvest index (HI).In contrast,the EP genotype exerted a negative effect on thousand-grain weight (KGW).The ratio of the performance of the EP genotype relative to the NEP genotype in terms of yield and total biomass correlated positively with mean daily solar radiation during a 40-day period around heading.These results indicate that the effectiveness of the EP genotype depends on the availability of solar radiation,and the effect of this genotype is consistently positive for sink formation,conditional in terms of source capacity,and positive in a high-radiation environment.

Influence of Epistasis and QTL×Environment Interaction on Heading Date of Rice(Oryza sativa L.)

QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.

Characterization of early maturing elite genotypes based on MTSI and MGIDI indexes:an illustration in upland cotton(Gossypium hirsutum L.)

Background Globally,the cultivation of cotton is constrained by its tendency for extended periods of growth.Early maturity plays a potential role in rainfed-based multiple cropping system especially in the current era of climate change.In the current study,a set of 20 diverse Gossypium hirsutum genotypes were evaluated in two crop seasons with three planting densities and assessed for 11 morphological traits related to early maturity.The study aimed to identify genotype(s)that mature rapidly and accomplish well under diverse environmental conditions based on the two robust multivariate techniques called multi-trait stability index(MTSI)and multi-trait genotype-ideotype distance index(MGIDI).Results MTSI analysis revealed that out of the 20 genotypes,three genotypes,viz.,NNDC-30,A-2,and S-32 accomplished well in terms of early maturity traits in two seasons.Furthermore,three genotypes were selected using MGIDI method for each planting densities with a selection intensity of 15%.The strengths and weaknesses of the genotypes selected based on MGIDI method highlighted that the breeders could focus on developing early-maturing genotypes with specific traits such as days to first flower and boll opening.The selected genotypes exhibited positive genetic gains for traits related to earliness and a successful harvest during the first and second pickings.However,there were negative gains for traits related to flowering and boll opening.Conclusion The study identified three genotypes exhibiting early maturity and accomplished well under different planting densities.The multivariate methods(MTSI and MGIDI)serve as novel approaches for selecting desired genotypes in plant breeding programs,especially across various growing environments.These methods offer exclusive benefits and can easily construe and minimize multicollinearity issues.

Agronomic Performance, Stability Analysis and Evaluation of Anthracnose Disease Resistance of Common Bean Lines Derived by Marker-Assisted Backcrossing in Uganda

The present study focused on evaluating the agronomic performance, stability, and anthracnose resistance of common bean lines derived through Marker-Assisted Backcrossing in Uganda. Eight marker-assisted selection (MAS) backcross-derived bush bean lines with red seed types, alongside two checks, were evaluated in a randomized complete block design replicated two times in five locations for three consecutive crop-growing seasons in 2021 and 2022. The study aimed to identify lines with both high stable yields and enhanced resistance to anthracnose disease for potential release and utilization in future bean varietal development in Uganda. Agronomic traits, including days to 50% flowering, days to 90% physiological maturity, seed yield, seed yield components, and anthracnose disease reaction under natural infestation were assessed. The response to anthracnose disease was further assessed using six isolates of Colletotrichum lindemuthianum representing six different races. Results indicated that the agronomic performances of the MAS backcross-derived bush bean lines were statistically comparable to the recurrent parent NABE14. Specifically, six lines exhibited statistically equal to or higher performance than NABE14 in terms of seed yield, total number of seeds and number of pods per plant. The combined analysis of variance for seed yield showed significant (p Co-42 and Co-5 anthracnose resistance genes in the derived line. In conclusion, UGKT-B157-4, identified as the best-performing and stable genotype, demonstrates promise for release and use in future bean varietal development in Uganda, offering a combination of high yields and enhanced anthracnose disease resistance. The study provides valuable insights into the potential of Marker-Assisted Backcrossing in improving common bean varieties in the region.

Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai＇an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions （QEs）. Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rhtl and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection （MAS）.

Genetic and Genotype × Environment Interaction Effects for Appearance Quality of Rice

This study was conducted to generate genetic information in rice varieties based on a complete diallel crosses over two years. The results indicated that genotype effect was significant for all traits. Genotype × environment interaction effects were significant only for cooked grain length （CGL） and cooked grain shape （CGSH）. General combining ability （GCA） and specific combining ability （SCA） effects were significant for entire traits, which indicated the important roles of both additive and non-additive gene actions. GCA x environment interaction effects were significant for CGL, CGSH and grain elongation index （GEI）. In the controlling of the inheritance of milled grain shape （GSH）, milled grain width （MGW）, GEI, milled grain length （MGL）, CGSH and cooked grain width （CGW）, the additive gene effects were more important than non-additive one. The average degree of dominance was within the range of partial dominance for all of the traits. The narrow-sense heritability was ranged from 0.65 （GSH） to 0.36 （CGL）. GCA effects were significant for all of the parents in milled grain length and it was significant for some of the parents in other traits. The crosses of Deilmani × IRFAON-215 exhibited significant SCA for GEI. The positive mean of heterosis was observed for CGW. The highest maximum values of heterosis were revealed in GEI, flowed by GSH, MGW and CGW. GCA and MPV were significantly and positively correlated together for all traits.

A holistic framework for facilitating environmental and human health

In the Anthropocene,health is necessary to achieve global sustainable development.This is a challenge because health issues are complex and span from humans to ecosystems and the environment through dynamic interac-tions across scales.We find that the health issues have been mainly addressed by disciplinary endeavors which unfortunately will not result in panoramic theories or effective solutions.We recommend focusing on the intri-cate interactions between humans,ecosystems and the environment for developing common theoretical under-standings and practical solutions for safeguarding planetary health,with human health as the key indicator and endpoint.To facilitate this paradigm shift,a holistic framework is formulated that incorporates disturbances from inner Earth and our solar system,and accommodates interactions between humans,ecosystems and the environ-ment in a nested hierarchy.An integrative and transdisciplinary health science is advocated along with holistic thinking to resolve our current health challenges and to achieve the health-related sustainable development goals.

Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia

To explore the effect of genotype and genotype x environment interaction on Fe concentration in rice grains, Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007-2008 using the AMMI-biplot method. Experiments were conducted using a randomized completely block design with three replications in eight environments. Results indicated that environment （E）, genotype （G） and genotype x environment interaction （GE） significantly affected Fe concentration in rice grains. Environment explained 74.43 % of total （G＋E＋GE） variation, whereas G and GE captured 5.60% and 19.67%, respectively. Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains. Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.

Gene×environment interaction in major depressive disorder

Major depressive disorder(MDD)is a multifactorial disorder,where multiple susceptibility genes interact with environmental factors,predisposing individuals to the development of the illness.In this article,we reviewed different gene×environment interaction(G×E)studies shifting from a candidate gene to a genome-wide approach.Among environmental factors,childhood adversities and stressful life events have been suggested to exert crucial impacts on MDD.Importantly,the diathesis-stress conceptualization of G×E has been challenged by the differential susceptibility theory.Finally,we summarized several limitations of G×E studies and suggested how future G×E studies might reveal complex interactions between genes and environments in MDD.

Genotype x Environment Interaction of Carotene Content of Yellow-Fleshed Cassava Genotypes in Nigeria

Cassava is an important starchy root crop and a major staple for more than 70 million people in Nigeria. New yellow-fleshed genotypes are being developed to combat vitamin A deficiency. Trials of 18 yellow-fleshed genotypes and two officially released white-fleshed clones, used as checks for 2008/2009 and 2009/2010 seasons in five major cassava growing agroecological zones of Nigeria. The trial locations were Ikenne （humid forest）, Ibadan （forest-savanna transition）, Ubiaja （subhumid forest）, Mokwa （southern Guinea savanna） and Zaria （northern Guinea savanna）. At each location, the trial was established in a randomized complete block design with four replications. The objective of the study was to assess genotype performance and genotype ~ environment interaction for total carotene concentration （TCC）, total carotene content per root （TC-R）, and total carotene content per plant （TC-P）. Significant differences （P 〈 0.001） among genotypes, environments and genotype x environment interaction for all the traits evaluated were observed. For TCC, TC-R and TC-P, the best genotypes across the 10 environments were TMS I051601, TMS 1050311, and TMS 1050998. Variation among genotypes accounted for most of the Total Sum of Squares for TCC （67.9%）, TC-R （39.0%） and TC-P （35.9%）. These characteristics of total carotene were also highly correlated. This study revealed that cassava with total carotene concentration can be assessed using either the TCC, or the TC-R, or the TC-P.

A Method for Assessing the Interaction Environment of Organizations

This paper presents a method for assessing the influence of the interaction environment of an organization. The interaction environment of an organization is composed of three elements： （1） the physical structure of the organization, including numbers of buildings, floors, common gathering areas, size, industry, and physical layout; （2） the information structure, consisting of the numbers and types of communication channels in the organization; and （3） the social structure, consisting of both individual-level assessments of the social environment of the organization as well as the organizational attempts to create a more social environment. This assessment tool has been tested in a large-scale study of organ donation campaigns in 46 organizations. Findings from this earlier test of the assessment tool demonstrate that interaction environment influences the way people communicate about, seek information about, and make decisions about health-related topics in organizations. Additionally, the individual elements of the interaction environment work in complex ways and also influence communication patterns and knowledge about health information. This paper details the procedures for using this assessment tool, methods for analyzing the findings, limitations of the tool, and areas in need of refinements and further researches.

AMMI analysis of interaction of genotype and environment in chalkiness of indica rice

Chalkiness is an unpleasant trait for rice con-sumer,which is known to be controlled geneti-cally and affected by environment during grainmaturing.We used the model of Additive Main

Variation and stability analysis of growth traits of poplar clones in the seedling stage in northeast China

Plant phenotypes are infl uenced by genetic and environmental factors.In this study,the growth traits of 43 one-year-old poplar clones grown at diff erent sites in northeast China(Dongling State-owned Forest Protection Center,DL;Baicheng State-owned forest farm,BC;and Cuohai Forest farm,CH)were evaluated and analyzed across clones and sites.Results show signifi cant diff erences in height and base diameter among sites and clones.Phenotypic and genetic variation coeffi cients ranged from 49.59%(BC)to 58.39%(DL)and from 49.33%(BC)to 58.06%(DL),respectively.Additive main eff ects and multiplicative interaction(AMMI)analysis showed that the eff ects of genotype,environment,and genotype×environment interaction were signifi cantly diff erent.Genetic variation was the main source of variation,accounting for 48.6%.AMMI biplot showed that clone 30 had high and stable yields at the three sites.From an evaluation of multiple traits and GGE biplot that clone 2,clone 30 and clone 25 had higher yield than the other clones at DL,CH and BC,respectively.These clones will provide material for forest regeneration in northeast China.

Genotype × environment interaction patterns of dry matter yield in meadow brome, orchardgrass, tall fescue, and timothy evaluated at harsh winter sites

Background:Genotype×environment interaction(GEI)slows genetic gains and complicates selection decisions in plant breeding programs.Forage breeding program seed sales often encompass large geographic regions to which the cultivars may not be adapted.An understanding of the extent of GEI in perennial,cool-season forage grasses will facilitate improved selection decisions and end-use in areas with harsh winters.Methods:We evaluated the dry matter yield of nine meadow brome(Bromus biebersteinii Roemer&J.A.Schultes),nine orchardgrass(Dactylis glomerata L.),seven tall fescue(Lolium arundinaceum(Schreb.)Darbysh.),and 10 timothy(Phleum pratense L.)cultivars or breeding populations at seven high latitude and/or elevation locations in Canada and the United States from 2019 to 2021.Results:For each of the species,we found significant differences among the genotypes for dry matter yield across environments and found significant levels of GEI.Using site regression analysis and GGE biplot visualizations,we then characterized the extent of the interactions in each species.Except for tall fescue,there was little evidence for the broad adaptation of genotypes across locations.Conclusions:This research adds further evidence to the limitations of perennial,forage breeding programs to develop widely adapted cultivars and the need to maintain regional breeding efforts.

Growth variations and stability analyses of seven poplar clones at three sites in northeast China

Growth characteristics have complex inheritance patterns and genotype(G) by environment(E) interaction make predicting tree response to environmental changes difficult.In this study,the growth of seven poplar clones at three different sites was taken as the research focus,and heights and basal diameters were investigated in the second growing season.An ANOVA showed that all main effects,site,clone number and their interactions were highly significant in the overall F-tests.The coefficients of variation and repeatability of different traits ranged from 15.5 to 43.9%and from 0.549 to 0.912,respectively.AMMI(Additive Main Effects and Multiplicative Interaction) analysis results showed that genotype,environment and G × E interaction were significantly highly correlated.The stability analysis indicated that different clones showed different growth traits on different sites,which suggests that elite clones should be selected separately for different sites.Based on the growth traits,under a 10% selection rate,three clones were selected for different sites and the genetic gains of growth traits ranged from 4.7 to 11.2%.The three selected clones could be used to establish plantations in the future in different sites.

Global Bioethical Prevention of the Collision of Biological and Cultural Evolution on Miserable Human Survival

With the cultural myth that science can only determine the way the world ＂is＂ （facts）, while humanities, social sciences, lawyers, philosophers, and theologians must determine the way the world ＂ought to be＂ （values）, those in position of global-, national-, and local-political power make major decisions of the use （or non-use） of scientific knowledge and technology. As a result, the human being has created a non-scientifically based cultural environment that is affecting his ability to survive. In effect, cultural evolution is occurring more rapidly than biological evolution that can adapt to the changes brought about in the physical and psycho-social environments. In a pluralistic cultural world, where each society has generated a different view of human nature and different ethical values, the use, misuse, or non-use of scientific and technological advances are derived from these unscientific views of human nature. Since all life depends on limiting interacting environmental and ecological factors, it is imperative that scientific information be used to govern how to minimize irreversible effects on life-sustaining ecological factors, but also scientific information bearing on understanding human nature ought to be integrated into a ＂global bioethics＂. While ethical values cannot be directly derived from scientific factors, it is also true that human values or our ＂ought＂ cannot be maintained in ignorance or defiance of the facts or the ＂is＂.

One compound approach combining factor-analytic model with AMMI and GGE biplot to improve multi-environment trials analysis

To improve multi-environmental trial(MET)analysis,a compound method—which combines factor analytic(FA)model with additive main effect and multiplicative interaction(AMMI)and genotype main effect plus genotype-by-environment interaction(GGE)biplot—was conducted in this study.The diameter at breast height of 36 open-pollinated(OP)families of Pinus taeda at six sites in South China was used as a raw dataset.The best linear unbiased prediction(BLUP)data of all individual trees in each site was obtained by fitting the spatial effects with the FA method from raw data.The raw data and BLUP data were analyzed and compared by using the AMMI and GGE biplot.BLUP results showed that the six sites were heterogeneous and spatial variation could be effectively fitted by spatial analysis with the FA method.AMMI analysis identified that two datasets had highly significant effects on the site,family,and their interactions,while BLUP data had a smaller residual error,but higher variation explaining ability and more credible stability than raw data.GGE biplot results revealed that raw data and BLUP data had different results in mega-environment delineation,test-environment evaluation,and genotype evaluation.In addition,BLUP data results were more reasonable due to the stronger analytical ability of the first two principal components.Our study suggests that the compound method combing the FA method with the AMMI and GGE biplot could improve the analysis result of MET data in Pinus teada as it was more reliable than direct AMMI and GGE biplot analysis on raw data.

Performance and yield stability of maize hybrids in stress-prone environments in eastern Africa

Identification and deployment of high-yielding and stress-tolerant maize hybrids adapted to stress-prone agro-ecologies is important for improving the food security and livelihoods of smallholder farmers in eastern Africa.The objectives of this study were to(i)assess the performance of maize hybrids under well-watered and drought stress conditions;(ii)evaluate grain yield stability of 65 intermediate-maturing and 55 early-maturing hybrids in 24 well-watered locations and seven drought stress locations;and(iii)identify representative and/or discriminative testing locations for increasing genetic gains for the target traits.There were significant differences for grain yield among early-and intermediatematuring hybrids tested under well-watered and drought stress environments.Among the early-maturing hybrids,the top 10 hybrids produced 46.8%–73.9%and 31.2%–42.1%higher mean grain yields than the best commercial check under drought and well-watered conditions,respectively.Among the intermediate-maturing hybrids,the top 10 hybrids produced 25.2%–47.7%and 8.5%–13.5%higher grain yield than commercial checks under drought stress and well-watered conditions,respectively,suggesting improvement in the levels of drought tolerance in both early-and intermediate-maturing hybrids.GGE biplot analysis and a bi-segmented regression linear method identified specific early-maturing and intermediate-maturing hybrids that performed well under both well-watered and drought stress conditions.These hybrids could be recommended for commercial production in eastern Africa.Kakamega in Kenya was found to be the most representative and highly discriminating site among well-watered testing locations,while Kabuku in Tanzania was the least representative of test locations.For testing under drought stress conditions,Kiboko in Kenya was identified as the most representative location.This information could be useful for allocating resources and streamlining CIMMYT maize hybrid testing in eastern Africa.

Investigation on Pasting Characteristics of Spring-sown Chinese Bread Wheats

Forty-seven spring wheat Triticumaestivum cultivars and advanced lines from spring-sown spring wheat regions, at twelve locations in 1998 and 1999, were used to investigate pasting properties of Chinese spring wheats. Starch pasting properties were closely associated with noodle quality. Significant differences were observed for all pasting characteristics. Samples collected from Harbin, Shenyang, Beijing, Ba-meng, Yongning, and Urumqi had better pasting quality than those from other locations. Genotype, environment, and genotype by environment interaction had large effects on all pasting characteristics. Significant correlations among pasting characteristics were observed and peak viscosity was considered the most important pasting characteristics.